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- PDB-1hnb: CRYSTAL STRUCTURE OF HUMAN CLASS MU GLUTATHIONE TRANSFERASE GSTM2... -

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Basic information

Entry
Database: PDB / ID: 1hnb
TitleCRYSTAL STRUCTURE OF HUMAN CLASS MU GLUTATHIONE TRANSFERASE GSTM2-2: EFFECTS OF LATTICE PACKING ON CONFORMATIONAL HETEROGENEITY
ComponentsGLUTATHIONE S-TRANSFERASE
KeywordsTRANSFERASE(GLUTATHIONE)
Function / homology
Function and homology information


nitrobenzene metabolic process / cellular detoxification of nitrogen compound / hepoxilin biosynthetic process / glutathione binding / regulation of skeletal muscle contraction by regulation of release of sequestered calcium ion / linoleic acid metabolic process / Glutathione conjugation / glutathione peroxidase activity / relaxation of cardiac muscle / positive regulation of ryanodine-sensitive calcium-release channel activity ...nitrobenzene metabolic process / cellular detoxification of nitrogen compound / hepoxilin biosynthetic process / glutathione binding / regulation of skeletal muscle contraction by regulation of release of sequestered calcium ion / linoleic acid metabolic process / Glutathione conjugation / glutathione peroxidase activity / relaxation of cardiac muscle / positive regulation of ryanodine-sensitive calcium-release channel activity / intercellular bridge / negative regulation of ryanodine-sensitive calcium-release channel activity / cellular response to caffeine / glutathione transferase / glutathione transferase activity / regulation of cardiac muscle contraction by regulation of the release of sequestered calcium ion / xenobiotic catabolic process / regulation of release of sequestered calcium ion into cytosol by sarcoplasmic reticulum / glutathione metabolic process / sarcoplasmic reticulum / fatty acid binding / signaling receptor binding / enzyme binding / protein homodimerization activity / extracellular exosome / cytosol / cytoplasm
Similarity search - Function
Glutathione S-transferase, Mu class / : / Glutathione S-transferase, C-terminal domain / Glutathione S-transferase, N-terminal domain / Glutathione transferase family / Glutathione S-transferase, C-terminal / Glutathione S-transferase Yfyf (Class Pi); Chain A, domain 2 - #10 / Glutathione S-transferase Yfyf (Class Pi); Chain A, domain 2 / Glutathione S-transferase, C-terminal-like / Soluble glutathione S-transferase C-terminal domain profile. ...Glutathione S-transferase, Mu class / : / Glutathione S-transferase, C-terminal domain / Glutathione S-transferase, N-terminal domain / Glutathione transferase family / Glutathione S-transferase, C-terminal / Glutathione S-transferase Yfyf (Class Pi); Chain A, domain 2 - #10 / Glutathione S-transferase Yfyf (Class Pi); Chain A, domain 2 / Glutathione S-transferase, C-terminal-like / Soluble glutathione S-transferase C-terminal domain profile. / Soluble glutathione S-transferase N-terminal domain profile. / Glutathione S-transferase, N-terminal / Glutathione S-transferase, C-terminal domain superfamily / Glutaredoxin / Glutaredoxin / Thioredoxin-like superfamily / Up-down Bundle / 3-Layer(aba) Sandwich / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
GLUTATHIONE S-(2,4 DINITROBENZENE) / Glutathione S-transferase Mu 2
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / Resolution: 3.5 Å
AuthorsRaghunathan, S. / Chandross, R.J. / Kretsinger, R.H. / Allison, T.J. / Penington, C.J. / Rule, G.S.
Citation
Journal: J.Mol.Biol. / Year: 1994
Title: Crystal structure of human class mu glutathione transferase GSTM2-2. Effects of lattice packing on conformational heterogeneity.
Authors: Raghunathan, S. / Chandross, R.J. / Kretsinger, R.H. / Allison, T.J. / Penington, C.J. / Rule, G.S.
#1: Journal: Biochemistry / Year: 1992
Title: Mapping of the Substrate-Binding Site of a Human Class Mu Glutathione Transferase Using Nuclear Magnetic Resonance Spectroscopy
Authors: Penington, C.R. / Rule, G.S.
#2: Journal: Proc.Natl.Acad.Sci.USA / Year: 1991
Title: Cloning, Expression, and Characterization of a Class Mu Glutathione Transferase from Human Muscle, the Product of the Gst4 Locus
Authors: Vorachek, W.R. / Pearson, W.R. / Rule, G.S.
History
DepositionOct 15, 1993Processing site: BNL
Revision 1.0Jan 31, 1994Provider: repository / Type: Initial release
Revision 1.1Mar 24, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Feb 7, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.process_site / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: GLUTATHIONE S-TRANSFERASE
B: GLUTATHIONE S-TRANSFERASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)52,1604
Polymers51,2132
Non-polymers9472
Water00
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3960 Å2
ΔGint-17 kcal/mol
Surface area20120 Å2
MethodPISA
Unit cell
Length a, b, c (Å)57.000, 86.080, 105.850
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121
Atom site foot note1: CIS PROLINE - PRO A 60 / 2: CIS PROLINE - PRO B 38 / 3: CIS PROLINE - PRO B 60

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Components

#1: Protein GLUTATHIONE S-TRANSFERASE


Mass: 25606.422 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / References: UniProt: P28161, glutathione transferase
#2: Chemical ChemComp-GDN / GLUTATHIONE S-(2,4 DINITROBENZENE)


Mass: 473.415 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C16H19N5O10S
Nonpolymer detailsALTHOUGH CRYSTALS WERE GROWN IN THE PRESENCE OF GLUTATHIONE S-(2,4 DINITROBENZENE), ONLY THE ...ALTHOUGH CRYSTALS WERE GROWN IN THE PRESENCE OF GLUTATHIONE S-(2,4 DINITROBENZENE), ONLY THE GLUTATHIONE PORTION HAS OBSERVABLE DENSITY. COORDINATES ARE REPORTED FOR THE GLUTATHIONE PORTION ONLY (RESIDUE GDN).

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 2.53 Å3/Da / Density % sol: 51.46 %
Crystal grow
*PLUS
Temperature: 18 ℃ / Method: vapor diffusion, hanging drop / PH range low: 7.4 / PH range high: 6.8
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDDetails
1130 mg/mlenzyme1drop0.18 ml
21 MGS-DNB1drop0.0156 ml
3150 mMTris-HCl1reservoir
45 mMBME1reservoir
525-30 %PEG10001reservoir

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Data collection

RadiationScattering type: x-ray
Radiation wavelengthRelative weight: 1
Reflection
*PLUS
Highest resolution: 3.5 Å / Num. obs: 6732 / % possible obs: 95 % / Redundancy: 2.9 % / Num. measured all: 19494 / Rmerge(I) obs: 0.084 / Biso Wilson estimate: 11.35 Å2
Reflection shell
*PLUS
Mean I/σ(I) obs: 7.8

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Processing

Software
NameClassification
X-PLORmodel building
X-PLORrefinement
X-PLORphasing
RefinementResolution: 3.5→10 Å / σ(F): 0
Details: THE ELECTRON DENSITY FOR RESIDUES 203 - 217 IS POORLY DEFINED. THE TEMPERATURE FACTORS WERE NOT REFINED TO CONVERGENCE.
RfactorNum. reflection
Rwork0.207 -
obs0.207 6408
Refinement stepCycle: LAST / Resolution: 3.5→10 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3608 0 40 0 3648
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_bond_d0.007
X-RAY DIFFRACTIONx_bond_d_na
X-RAY DIFFRACTIONx_bond_d_prot
X-RAY DIFFRACTIONx_angle_d
X-RAY DIFFRACTIONx_angle_d_na
X-RAY DIFFRACTIONx_angle_d_prot
X-RAY DIFFRACTIONx_angle_deg1.31
X-RAY DIFFRACTIONx_angle_deg_na
X-RAY DIFFRACTIONx_angle_deg_prot
X-RAY DIFFRACTIONx_dihedral_angle_d
X-RAY DIFFRACTIONx_dihedral_angle_d_na
X-RAY DIFFRACTIONx_dihedral_angle_d_prot
X-RAY DIFFRACTIONx_improper_angle_d
X-RAY DIFFRACTIONx_improper_angle_d_na
X-RAY DIFFRACTIONx_improper_angle_d_prot
X-RAY DIFFRACTIONx_mcbond_it
X-RAY DIFFRACTIONx_mcangle_it
X-RAY DIFFRACTIONx_scbond_it
X-RAY DIFFRACTIONx_scangle_it
Software
*PLUS
Name: X-PLOR / Classification: refinement
Refinement
*PLUS
Num. reflection all: 6408 / Rfactor obs: 0.207 / Rfactor Rwork: 0.207
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Type: x_angle_d / Dev ideal: 1.31

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